The Army Corps of Engineers, whose 100-plus workers occupy two buildings at the 186-year-old military post, says that the majority of its employees will have an easier time getting to new digs on Varick Street, and it doesn’t mind raising its annual rent from the $130,000 it pays in Brooklyn to the $1 million-plus in Manhattan.

But Borough President Markowitz said it’s incomprehensible that the Corps would want to leave the borough.

“To think that they want to leave Fort Hamilton for the outer borough of Manhattan?” Markowitz cried. “Fort-geddaboudit!”

But the Corps says it needs to be closer to its clients.

“Being in Manhattan will make it easier for us to travel to our customers, and for our customers to travel to us,” said Corps spokesman Justin Ward. “Fort Hamilton is a little hard to get to.”

Fort advocates fear that losing the Corps could be the first step in a process that would eventually close the base. In 2005, the Army’s Base Realignment Closure Committee considered shuttering Fort Hamilton, but decided against it partly because of the Corps’ presence. The committee’s next round of closure recommendations will be in 2015, and without the Corps on base, the waterfront installation is more vulnerable to ax-wielding bean counters.

“[The Corps’ departure] will diminish our military significance and that’s the only thing that counts,” said Bill Guarinello, chairman of the Fort Hamilton Citizens Action Committee.

Less than five employees of the Corps live in the Bay Ridge area, according to Ward, but that doesn’t mean the neighborhood is willing to give up it up without a fight.

“This flag will not be moved — not on my watch,” said Rep. Michael Grimm (R–Bay Ridge), a former Marine. “If their troops have issues, we’re going to do what we can to alleviate those issues and support them.”

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